module load python/3.10.9-fasrc01
source activate env_name
for f in exp1_foralign/*.fastq; # the loop will be run if the job on the single fastq file runs successfully
do rsem-calculate-expression --seed-length 16 --single-cell-prior --quiet --bowtie2 $f bowtie2_wcre exp1_align_res/"${f##*/}";
while (( $(jobs -p | wc -l) >= SLURM_CPUS_ON_NODE )); do wait -n; done 
done
conda deactivate